Sadhika Malladi
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/EMDomics |
| Branch: RELEASE_3_8 |
| Last Commit: cf2c6f2 |
| Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:25:23 -0400 (Sat, 13 Apr 2019).
| Package 466/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EMDomics 2.12.0 Sadhika Malladi
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: EMDomics |
| Version: 2.12.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EMDomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EMDomics_2.12.0.tar.gz |
| StartedAt: 2019-04-13 02:02:06 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:05:08 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 182.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: EMDomics.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EMDomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EMDomics_2.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/EMDomics.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EMDomics/DESCRIPTION' ... OK
* this is package 'EMDomics' version '2.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'EMDomics' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOMPIhy/R.INSTALL19207aed33a1/EMDomics/man/calculate_emd.Rd:101: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOMPIhy/R.INSTALL19207aed33a1/EMDomics/man/calculate_emd_gene.Rd:31: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOMPIhy/R.INSTALL19207aed33a1/EMDomics/man/calculate_emd_gene.Rd:47: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/EMDomics.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre]
Daniel Schmolze <emd@schmolze.com> [aut, cre]
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cvm_pairwise_q: no visible global function definition for 'combn'
.cvm_pairwise_q : <anonymous>: no visible global function definition
for 'median'
.emd_gene_pairwise: no visible global function definition for 'hist'
.emd_pairwise_q: no visible global function definition for 'combn'
.emd_pairwise_q : <anonymous>: no visible global function definition
for 'median'
.ks_pairwise_table: no visible global function definition for 'ks.test'
calculate_cvm: no visible global function definition for 'combn'
calculate_cvm : <anonymous>: no visible global function definition for
'median'
calculate_cvm_gene: no visible global function definition for 'combn'
calculate_emd: no visible global function definition for 'combn'
calculate_emd : <anonymous>: no visible global function definition for
'median'
calculate_emd_gene: no visible global function definition for 'combn'
calculate_ks: no visible global function definition for 'combn'
calculate_ks : <anonymous>: no visible global function definition for
'p.adjust'
calculate_ks : <anonymous>: no visible global function definition for
'median'
calculate_ks_gene: no visible global function definition for 'combn'
calculate_ks_gene: no visible global function definition for 'ks.test'
Undefined global functions or variables:
combn hist ks.test median p.adjust
Consider adding
importFrom("graphics", "hist")
importFrom("stats", "ks.test", "median", "p.adjust")
importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_cvm_density 6.67 0.00 6.67
calculate_cvm 5.78 0.00 5.80
plot_cvmperms 5.71 0.05 5.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_cvm_density 7.75 0.02 7.76
plot_cvmperms 6.31 0.00 6.32
calculate_cvm 6.00 0.03 6.03
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/EMDomics.Rcheck/00check.log'
for details.
EMDomics.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/EMDomics_2.12.0.tar.gz && rm -rf EMDomics.buildbin-libdir && mkdir EMDomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EMDomics.buildbin-libdir EMDomics_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL EMDomics_2.12.0.zip && rm EMDomics_2.12.0.tar.gz EMDomics_2.12.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 96611 100 96611 0 0 2303k 0 --:--:-- --:--:-- --:--:-- 2549k
install for i386
* installing *source* package 'EMDomics' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'EMDomics'
finding HTML links ... done
CVMomics html
EMDomics html
KSomics html
calculate_cvm html
calculate_cvm_gene html
calculate_emd html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOMPIhy/R.INSTALL19207aed33a1/EMDomics/man/calculate_emd.Rd:101: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
calculate_emd_gene html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOMPIhy/R.INSTALL19207aed33a1/EMDomics/man/calculate_emd_gene.Rd:31: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpOMPIhy/R.INSTALL19207aed33a1/EMDomics/man/calculate_emd_gene.Rd:47: file link 'emd2d' in package 'emdist' does not exist and so has been treated as a topic
calculate_ks html
calculate_ks_gene html
emdomics-package html
plot_cvm_density html
plot_cvmnull html
plot_cvmperms html
plot_emd_density html
plot_emdnull html
plot_emdperms html
plot_ks_density html
plot_ksnull html
plot_ksperms html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'EMDomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EMDomics' as EMDomics_2.12.0.zip
* DONE (EMDomics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'EMDomics' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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EMDomics.Rcheck/examples_i386/EMDomics-Ex.timings
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EMDomics.Rcheck/examples_x64/EMDomics-Ex.timings
|